The use of frozen semen to minimize inbreeding in small populations

In this study, we compared the average coancestry and inbreeding levels for two genetic conservation schemes in which frozen semen from a gene bank is used to reduce the inbreeding in a live population. For a simple scheme in which only semen of generation-0 (G0) sires is used, the level of inbreeding asymptotes to 1/(2N), where N is the number of newborn sires in the base generation and rate of inbreeding goes to zero. However, when only sires of G0 are selected, all genes will eventually descend from the founder sires and all genes from the founder dams are lost. We propose an alternative scheme in which N sires from generation 1 (G1), as well as the N sires from G0, have semen conserved, and the semen of G0 and G1 sires is used for dams of odd and even generation numbers, respectively. With this scheme, the level of inbreeding asymptotes to 1/(3N) and the genes of founder dams are also conserved, because 50% of the genes of sires of G1 are derived from the founder dams. A computer simulation study shows that this is the optimum design to minimize inbreeding, even if semen from later generations is available

Managing inbreeding in selection and genetic conservation schemes of livestock

This thesis deals with the definition of selection and mating criteria for animal breeding populations under selection and for genetic conservation populations, especially emphasizing on populations with small effective sizes that have known pedigrees.The thesis can be divided into four main parts. Firstly, Chapters 2 and 3 deal with selection algorithms that manageDF for populations under selection with overlapping generations and random mating. Secondly, Chapters 4 and 5 deal with non-random mating schemes in combination with selection algorithms for discrete and overlapping generation structures, respectively. Thirdly, Chapters 6 and 7 deal with algorithms that minimizeDF in small and endangered populations. In Chapter 6,DF is minimized for populations with overlapping generations. In Chapter 7,DF is further reduced by using frozen semen of sires from the less related base population. Fourthly, Chapter 8 deals with methods to select against genetic defects while restrictingDF in populations with increased frequency of diseased alleles. CHAPTERS 2 AND 3In Chapter 2, a method is presented that maximizes the genetic merit of the selected animals while limiting the average coancestry of a population with overlapping generations after the current round of selection. For populations with overlapping generations, account has to be taken for previous and future use of animals of certain age-classes. Contributions within and over age-class were found by iteration. Inputs are Best Linear Unbiased Predicted (BLUP) breeding values of the selection candidates, and the relationship matrix of all animals. Output is the optimal number of offspring of each candidate. Computer simulations of dairy cattle nucleus schemes showed that the predefined rate of inbreeding was achieved. At the same rates of inbreeding, the dynamic selection method obtained up to 44% more genetic gain than truncation selection for BLUP breeding values. The advantage of the dynamic method over BLUP selection decreased with increasing population size and with less stringent restriction on inbreeding. In Chapter 3, the method of Chapter 2 was compared to a similar method that firstly optimized the distribution of parents within and thereafter over age classes per sex. It yielded significantly lower annual genetic gain, fewer animals selected and longer generation intervals, but maintained the rate of inbreeding closer to its constraint. The use of conventional relationships and of augmented relationships, which do not depend on the level of inbreeding, resulted in very similar breeding schemes, but the use of augmented relationships avoids correction of the current level of inbreeding. When optimising per generation, the generation interval was shorter compared to a scheme where an analogous annual restriction was in place and the annual rate of genetic gain was higher.CHAPTER 4 AND 5In Chapter 4, the effect of non-random mating on genetic gain was compared for populations with discrete generations. Mating followed a selection step where the average coancestry of selected animals was constrained, while genetic gain was maximized. Minimum coancestry (MC), Minimum coancestry with a maximum of one offspring per full-sib family (MC1) and Minimum variance of the relationships of the offspring (MVRO) mating schemes resulted in a delay in inbreeding of about two generations compared to Random, Factorial and Compensatory mating. At the sameDF , genetic gain was up to 22% higher for the MC1 and MVRO schemes compared to Random mating schemes. The effect of non-random mating was largest for small schemes or for schemes with a stringent restriction onDF.MC1 yielded the highest genetic gain in almost all selection schemes, with a lower computational cost than MVRO. In Chapter 5, MC1 mating scheme was compared with random mating schemes for populations with overlapping generations and a restriction onDF . When sires were progeny tested, these progeny tested bulls were selected instead of the young bulls, which lead to increased generation intervals, increased selection intensity of bulls and increased genetic gain (35% compared to a scheme without progeny testing). The effect of MC1 decreased for schemes with progeny testing. MC1 mating increased genetic gain 11-18% for overlapping and 1-4% for discrete generations, when schemes with similar rate of inbreeding and genetic gain per generation were compared. CHAPTER 6 AND 7In Chapter 6, a method that minimizes the increase of coancestry of parents and optimizes the contribution of each selection candidate for populations with overlapping generations is presented. When survival rate equalled 100%, only animals from the oldest age class were selected, which maximized the number of parents per generation, slowed down the turn over of generations and minimized the increase of coancestry across sublines. However, the population became split into sublines separated by age classes, which substantially increased inbreeding within sublines. Sublines were prevented by a restriction of selecting at least one sire and one dam from the second oldest age class, which resulted in an L times lowerDF , where L equals the average generation interval of sires and dams. Minimum coancestry mating resulted in lower levels of inbreeding than random mating, butDF was approximately the same or somewhat higher. For schemes where only the oldest animals were selected,DF increased with 18-52% compared with the proposed method. In Chapter 7, the advantage on the average coancestry level of selecting not only the least related sires from the oldest age-class, but also sires from the second oldest age-class is presented. By selecting sires from generation zero only, all genes will eventually descend from the founder sires and all genes from the founder dams are lost. By selecting sires from generation zero and one alternatively, also some genes of the founder dams will be conserved and the average coancestry level was approximately 20% lower than for a scheme, where only the oldest sires were used. TheDF was zero at equilibrium for both schemes. Dams could be used for one generation and sires unlimited, because the amount of frozen semen very large relative to the small population sires. Population size was 6, 10 and 20 and the schemes were symmetric with respect to the sexes. CHAPTER 8Increased inbreeding will result in increased frequency of detrimental alleles. In Chapter 8, different genetic models and evaluation systems to select against a genetic disease in populations with discrete generations are compared. When using optimum contribution selection with a restriction onDF of 1.0% to select against a single gene, selection directly on DNA-genotypes needed 2.0 generations to half the frequency of the disease allele with additive effects and a population with 100 new-born animals. When only phenotypic records were available, selection on BLUP or on genotype probabilities calculated by segregation analysis (SEGR) needed 1.0 or 2.0 generations longer to half the frequency of the disease allele when allele effects were additive or recessive, respectively. Smaller schemes or schemes with a more stringent restriction onDF needed more generations to half the frequency of the diseased allele or the fraction of diseased animals. SEGR and BLUP were approximately equally efficient under both single gene and polygenic inheritance models, suggesting that efficient selection against a disease is possible without knowing its mode of inheritance.In conclusion, by taking account of the relationships of the selected group of selected animals, inbreeding is controlled in the selection and mating criteria presented in this thesis. This principle was extended to populations with overlapping generations, which makes the methods useful for practical selection and genetic conservation populations with known pedigree. Only in well-controlled breeding schemes, the optimum contributions of each selection candidate will be realized, some deviations may be corrected in later rounds of selection. The optimized contributions and thus also the restriction onDF affected the structure of the breeding schemes, e.g. whether progeny tested animals were selected or not. In general, older and more parents were selected with a more stringent selection onDF . Due to such dynamic adaptations of the breeding schemes, genetic gain reduced only little whenDF was lowered. Non-random mating can improve the family structure of the population under selection, thereby further increase the genetic gain. For the genetic conservation schemes, the contributions per family could not become completely equalized, because of the overlapping structure of the generations, resulting in a level of average coancestry being somewhat higher than the theoretical minimum. Use of frozen semen from sires of the oldest generations could reduceDF to zero and reduce the average level of coancestry in combined in situ / ex situ conservation schemes

Genomic, Marker-Assisted, and Pedigree-BLUP Selection Methods for β-Glucan Concentration in Elite Oat

β-glucan, a soluble fiber found in oat (Avena sativa L.) grain, is good for human health, and selection for higher levels of this compound is regarded as an important breeding objective. Recent advances in oat DNA markers present an opportunity to investigate new selection methods for polygenic traits such as β-glucan concentration. Our objectives in this study were to compare genomic, marker-assisted, and best linear unbiased prediction (BLUP)–based phenotypic selection for short-term response to selection and ability to maintain genetic variance for β-glucan concentration. Starting with a collection of 446 elite oat lines from North America, each method was conducted for two cycles. The average β-glucan concentration increased from 4.57 g/100 g in Cycle 0 to between 6.66 and 6.88 g/100 g over the two cycles. The averages of marker-based selection methods in Cycle 2 were greater than those of phenotypic selection (P \u3c 0.08). Progenies with the highest β-glucan came from the marker-based selection methods. Marker-assisted selection (MAS) for higher β-glucan concentration resulted in a later heading date. We also found that marker-based selection methods maintained greater genetic variance than did BLUP phenotypic selection, potentially enabling greater future selection gains. Overall, the results of these experiments suggest that genomic selection is a superior method for selecting a polygenic complex trait like β-glucan concentration

Genetic parameters of fillet fatty acids and fat deposition in gilthead seabream (Sparus aurata) using the novel 30 k Medfish SNP array

Lipid-related traits are important candidates for a breeding goal for gilthead seabream, because they affect both fish and human health, as well as production efficiency. However, to date there have been very few estimates of genetic parameters for these traits, and the genetic relationship between fatty acids and other important traits have never been reported for gilthead seabream. Therefore, the aim of this study was to estimate genomic heritability and genetic relationships of fat deposition traits and individual muscle fatty acids in a commercial population of gilthead seabream using the novel ~30 k MedFish SNP array. In total 967 gilthead seabream fed with a commercial feed were genotyped with the MedFish SNP chip which included ~30 K informative markers for this species. On average, the fish weighed 372 g. The mean content of eicosapentaenoic acid (EPA) + docosahexaenoic acid (DHA) was 822 mg per 100 g fillet. The heritability of muscle fat, viscera weight and percentage viscera were in the range of 0.34–0.46. The genetic correlation of body weight with muscle fat was 0.12, indicating that genetic variation in muscle fat is largely independent of the weight of the fish. The heritability of the product of endogenous fatty acid synthesis (n = 240), palmitoleic acid (16:1n-7), was high (0.43). The estimated heritability of EPA (%) and DHA (%) was 0.39 and 0.33, respectively. Both EPA and DHA had low, non-significant genetic correlations with body weight, and DHA had a negative genetic correlation with muscle fat (−0.53). It is possible to increase EPA and DHA content in gilthead seabream fillets by selective breeding. The high heritability of 16:1n-7, a marker of de novo lipogenesis, suggests that there is a strong genetic component to this metabolic pathway in gilthead seabream. Muscle fat deposition and body weight seem to be independent traits, and selective breeding for faster growth is not likely to influence the proportional content of EPA and DHA

Non-random mating schemes for selection with restricted rates of inbreeding

Modern livestock breeding programs feature accurate breeding value estimation and advanced reproductive technology. Such programs lead to rapid genetic progress, but they also lead to the accumulation of inbreeding via heavy impact of a few selected individuals or families. Inbreeding rates are accelerating in most species, and economic losses due to inbreeding depression in production, growth, health, and fertility are a serious concern. Most research has focused on preservation of rare breeds or maintenance of genetic diversity within closed nucleus breeding schemes. However, the apparently large population size of many livestock breeds is misleading, because inbreeding is primarily a function of selection intensity. Strategies for maintaining variation by restricting relationships between selected animals or by artificially increasing the emphasis on within-family information when estimating breeding values have been suggested, and some approaches seem to provide greater long-term responses than BLUP selection. Corrective mating programs are widely used in some species, and these can be modified to consider selection for economic merit adjusted for inbreeding depression. Selection of parents of AI bulls based on optimal genetic contributions to future generations, which are a function of estimated breeding values and genetic relationships between selected individuals, appears most promising. Rapid implementation of such procedures is necessary to avoid further reductions in effective population size. Missing pedigree information is a problem in practice, and the low net present value of future genetic gains makes it difficult for breeding companies to sacrifice short-term economic gains in favor of long-term diversity issues

Minimization of rate of inbreeding for populations with overlapping generations combining live and frozen genetics

Minimization of rate of inbreeding for populations with overlapping generations combining live and frozen genetics each selection candidate. The carrying capacity of the population is limited to a fixed number of animals per year. For survival rates <100 % the algorithm has to optimize the use of few old and less related animals with many young and higher related animals. For a scheme where the oldest animals were selected, ∆F increased with 18-5 2% compared with the proposed method. When freezing semen of all sires in a gene bank and assuming that each sire can be used infinitely, the relationships are set in the first 2-3 years, and thereafter the average co-ancestry of the population stays about the same, such that ∆F is approximately zero. Thus, the relationships among the live animals converges to that of the cryo conserved sires. The level of inbreeding in the optimal schemes with 6 new-born animals per year (3 sires + 3 dams) is 0.060, which is lower than the expected level of inbreeding when simply the 3 founder sires were cryo conserved, i.e. this would result in an inbreeding coefficient of 0.083 (=1/(4*3). The latter implies that the optimal method also conserves genes of the founder dams by using frozen semen of their male offspring